If your map has hundreds or thousands of hexes, I would not recommend trying to render all of them in the mini-map; whether or not they can be batched, this is adding too much complexity/overhead to the minimap. Instead, consider rendering the map once to a render texture and displaying this texture in the minimap. Any dynamic content such as icons or markers should generally be drawn separately above the texture, not rendered into the texture.
As for how to render the texture, generally you would use a separate camera positioned above the map so that it can see the whole map, configured to only see the layer(s) that the map tiles are on. Make sure to disable this camera after the texture is rendered! If the minimap has a separate visual style, you'll need a separate copy of the map for rendering the minimap.
There are a few possible approaches, depending on how your minimap works:
Static Minimap
If the minimap shows the entire map at once, and the map tiles do not change, then you only need to render the map once, at the same resolution as the minimap. If the tiles change over time, then you might need to periodically re-render the map (this could potentially cause a noticeable momentary stutter, so you might need to be careful about when you do it).
Panning Minimap
If the minimap shows a limited portion of the overall map, you may be able to render the entire map into a texture and pan this around in the minimap window, masking the portion that is outside of the minimap's window. For example, if your minimap is 200x200 pixels and shows 10% of the overall map, then you could render the entire map at 2000x2000. Again, if your map tiles do not change, you would only need to render once, but if they change over time then you might need to re-render some or all of the minimap.
This approach may not be practical if the map is extremely large and a render of the full map would consume excessive texture memory.
Zoomable panning minimap
Some games with a panning minimap also let the user zoom the minimap in and out. This adds an additional layer of complexity. Depending on the needs of your game and how your zoom function works, you could potentially render the minimap at multiple resolutions, or render at the highest resolution and scale it up and down depending on the zoom level.
Additional tips
- If your game has fog of war, this might constantly change the appearance of the minimap. In this case, it may be better to render the fog of war as a separate effect above the map texture.